Gene Reports最新文献

{"title":"Mechanisms of resistance and decreased susceptibility to azithromycin in Shigella","authors":"","doi":"10.1016/j.genrep.2024.102011","DOIUrl":"10.1016/j.genrep.2024.102011","url":null,"abstract":"<div><p>Azithromycin (AZM) is a primary treatment for shigellosis in children and a secondary option for adults. However, <em>Shigella</em> spp., has increasingly developed resistance to multiple antibiotics, including AZM. This rise in AZM-induced resistance complicates treatment, particularly with the emergence of multi-drug resistant (MDR) strains and the inappropriate and excessive use of antibiotics. Moreover, various mechanisms contribute to the decreased susceptibility to azithromycin (DSA) in <em>Shigella</em> spp., often involving antimicrobial resistance genes harboring on mobile genetic elements. These mechanisms hinder efforts to control the spread of DSA-<em>Shigella</em> strains. Therefore, this review aims to discuss the mechanisms of AZM resistance in <em>Shigella</em> infections and shed light on the important mechanisms underlying DSA in <em>Shigella</em>.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141997514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autophagic genes and antioxidant status during doxorubicin therapy under temperature-stressed conditions in breast cancer cells","authors":"","doi":"10.1016/j.genrep.2024.102009","DOIUrl":"10.1016/j.genrep.2024.102009","url":null,"abstract":"<div><h3>Objectives</h3><p>Autophagy as a cellular event swings between apoptosis induction and cellular maintenance during chemotherapy. The interplay between autophagy and reactive oxygen species (ROS) remains obscure in cancer progression and treatment. This study aimed to determine the combination effect of chemotherapy and hyperthermia on cancer cell proliferation, autophagy signaling, and oxidative stress status.</p></div><div><h3>Methods</h3><p>To estimate the autophagic genes' role and antioxidant capacity involvement during chemotherapy, human breast cancer cell lines (MCF7 and CAL51) were exposed to a high temperature at 42 °C and treated with doxorubicin (DOX). The MTT assays were performed to determine the cell survival levels, and the autophagic gene expression levels (ATG5, LC3A, LC3B, and Beclin1) were analyzed. The intracellular TAS (total antioxidant status) and SOD (superoxide dismutase) activities were determined.</p></div><div><h3>Results</h3><p>The combined effects of high temperature with chemotherapy significantly reduced cell viability and cell survival compared to cells treated with the chemotherapeutic agent DOX alone. The cell's autophagic gene activities were significantly increased after exposure to 42 °C temperature and DOX-based chemotherapy compared to the cells treated with DOX alone. It was observed that TAS and SOD activities were increased in the cell lines exposed to high temperatures with DOX compared to the cells treated with DOX alone. Increased autophagic gene expression levels and cell death were observed in response to the high temperature and DOX treatment in breast cancer cells.</p></div><div><h3>Conclusion</h3><p>The study may provide a plausible route and treatment plan for the individual adoption of cancer chemotherapy and be developed as part of the personalized medicine protocol.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141964498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salivary levels of cell cycle regulatory proteins p53, cyclin D1, CDK 4 and protein carbonylation in post COVID-19 cohort – An observational study","authors":"","doi":"10.1016/j.genrep.2024.102010","DOIUrl":"10.1016/j.genrep.2024.102010","url":null,"abstract":"<div><h3>Background</h3><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is responsible for causing the coronavirus disease 2019 (COVID-19) pandemic that brought the world to a standstill in 2019, enters human cells by angiotensin-converting enzyme 2 (ACE2) receptors. The virus binds to ACE2 using the spike-like protein on its surface. ACE2 receptors also play an essential role in promoting the proliferation and invasion of oral squamous cell carcinoma (OSCC) cells by converting Angiotensin I, which binds to its type 1 or type 2 receptor inducing anti-apoptotic and anti-oxidative stress phenotypes. This study aimed to assess the long-term effects of SARS-CoV-2 by determining its effect on cell cycle regulatory proteins p53, cyclin D1, cyclin-dependent kinase 4 (CDK 4) and protein carbonylation in saliva.</p></div><div><h3>Objective</h3><p>To estimate and correlate the levels of p53, cyclin D1, CDK 4 and protein carbonylation measured at baseline and 6 months follow-up among post COVID-19 cohort.</p></div><div><h3>Method</h3><p>The study was conducted among 40 outpatients who were diagnosed with SARS-CoV-2 between January 2022 and February 2022. The study commenced after Institutional Ethics Committee clearance. The study comprised 40 post-COVID patients who were tested positive for COVID-19. Unstimulated whole saliva samples were collected from study participants by spitting method at baseline and 6 months. p53, cyclin D1, CDK 4 and protein carbonylation expression were assessed using ELISA. The obtained data were subjected to statistical analysis.</p></div><div><h3>Results</h3><p>The levels of proteins p53, cyclin D1, CDK 4 and protein carbonylation measured at baseline and six months were (687.02 ± 88.15 and 801.59 ± 82.72), (36.27 ± 5.04 and 45.71 ± 4.78), (9.25 ± 1.92 9.71 ± 0.98) and (864.76 ± 171.29 and 960.15 ± 82.03) respectively. There was a significant increase in levels of p53 (<em>p</em> &lt; 0.05), cyclin D1 (p &lt; 0.05), and protein carbonylation (p &lt; 0.05) from baseline to 6 months.</p></div><div><h3>Conclusion</h3><p>An increase in salivary levels of p53, cyclin D1, CDK 4 and protein carbonylation suggests that there may be long-term effects of SARS-CoV-2 on cell cycle regulatory proteins. Over-expression of these markers does not signify that these patients are likely to get OSCC in the future instead, there may be some retained long-term effects of the virus whose mechanism yet needs to be understood. Further, transcriptomic profiling of tumor suppressor proteins may give us interesting results on the long-term effects of SARS-CoV-2.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141990597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High levels of nucleotide diversity of a protein kinase gene, MAPK5 in populations of wild rice (Oryza rufipogon Griff.) from Thailand and Lao PDR","authors":"","doi":"10.1016/j.genrep.2024.102008","DOIUrl":"10.1016/j.genrep.2024.102008","url":null,"abstract":"<div><p>Protein kinase plays important roles in plant growth, development, and responses to various biotic and abiotic stresses. Levels of nucleotide diversity, however, have not been investigated to date in natural populations of wild rice. In this study, the diversity of the <em>MAPK5</em> gene and its characteristics were analyzed in samples of wild rice collected from natural populations in Thailand and Lao PDR, using a re-sequencing DNA technique. For the entire of 514 nucleotides sequence analyzed, non-synonymous, synonymous substitutions, and frame-shift indels were identified in coding sequence of exon1, but not for exon2. For non-coding sequences, indel mutations were present in the sequenced region of the first intron of the <em>MAPK5</em> gene. These results suggest that alternative splicing transcripts of the <em>MAPK5</em> gene are potentially generated in response to various environment factors. There was substantial nucleotide variation with a high estimate of nucleotide diversity (π = 0.18113), number of haplotypes (H = 15), and the number of polymorphic sites (S = 319). The Tajima's <em>D</em> value of the <em>MAPK5</em> gene was 1.673 (<em>p</em> &gt; 0.10), suggesting that the <em>MAPK5</em> gene of wild rice evolved neutrally. The high level of nucleotide diversity found in natural populations of wild rice may provide populations with the opportunity to adapt to environmental changes in their natural habitats.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141952929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent advances in molecular breeding and key insights into major pulse improvement efforts for sustainable food security","authors":"","doi":"10.1016/j.genrep.2024.101997","DOIUrl":"10.1016/j.genrep.2024.101997","url":null,"abstract":"<div><p>Pulses are important crops for global food security and are highly adaptable to diverse environmental conditions. Despite these merits, pulses often face neglect and undervaluation in production. Conventional breeding has been successful for centuries in improving various traits, based on their superior agronomic performance. However, this is a phenotype-based selection that is laborious, expensive, inefficient, error-prone, and often poorly adaptive. To address these challenges, molecular breeding has emerged as a valuable approach, bridging the gap between phenotype and genotype.</p><p>Consequently, we aimed to review recent advances in molecular breeding for major pulse crops, and the introgression of novel genes providing a comprehensive overview of breeding strategies for sustainable food security, particularly in developing countries. Genetic improvement through molecular breeding tools has been used to reliably improve pulse nutritional quality traits (such as taste, aroma, protein digestibility, essential amino acid profile, and the absence of anti-nutritional factors) and resistance to environmental stresses. Accordingly, the integration of next-generation genome sequencing, genome-wide association studies, high-throughput phenotyping, and omics research approaches are accelerating the discovery of the genetic loci underlying these traits and improving pulse research, mainly for key pulses like soybean, chickpea, broad bean, common bean, field pea, grass pea, cowpea, mung bean, and lentil. In general, molecular interventions in pulse breeding hold great promise for improving food and nutrition security, particularly in developing countries.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141962552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the Fluorion HCV QNP v3.0 real-time PCR assay for quantifying HCV RNA in Moroccan patients: A comparative study with COBAS AmpliPrep/COBAS TaqMan HCV v2.0","authors":"","doi":"10.1016/j.genrep.2024.102004","DOIUrl":"10.1016/j.genrep.2024.102004","url":null,"abstract":"<div><h3>Purpose</h3><p>Hepatitis C Virus (HCV) RNA quantification is crucial for diagnosing and monitoring chronic HCV treatment. Cost-effective methods are crucial to ensure accessibility. This study evaluated the Fluorion HCV QNP v3.0 Real-Time PCR assay's effectiveness in EDTA-plasma and serum, comparing it with the COBAS AmpliPrep/COBAS TaqMan HCV v2.0 (CAP/CTM HCV v2.0) test.</p></div><div><h3>Methods</h3><p>105 matched pairs of EDTA-plasma and serum specimens (91 positive and 14 negative) from HCV infected Moroccan patients were analyzed using the Fluorion HCV QNP v3.0 assay and compared to the CAP/CTM HCV v2.0 test, being the reference method.</p></div><div><h3>Results</h3><p>The values obtained by the Fluorion HCV QNP v3.0 in plasma were slightly higher than those in serum (3.94 ± 2.23 log₁₀ IU/mL versus 3.91 ± 2.22 log₁₀ IU/mL) and were both significantly lower than those quantified by the CAP/CTM HCV v2.0 assay (4.34 ± 2.28 log₁₀ IU/mL; <em>p</em> &lt; 0.001). High correlations were observed between the Fluorion HCV QNP v3.0 serum and CAP/CTM HCV v2.0 (R² = 0.9433), the Fluorion HCV QNP v3.0 plasma and CAP/CTM HCV v2.0 (R² = 0.949) and the Fluorion HCV QNP v3.0 serum and plasma (R² = 0.9954). HCV RNA was detected in all tested genotypes by both assays.</p></div><div><h3>Conclusion</h3><p>The Fluorion HCV QNP v3.0 assay demonstrated excellent performance in comparison with the CAP/CTM HCV v2.0 on both plasma and serum samples which can be used interchangeably for HCV quantification. The test was shown to be suitable for disease monitoring including all HCV genotypes.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141952619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity among Ethiopian sweet sorghum [Sorghum bicolor (L.) Moench] accessions using simple sequence repeat markers","authors":"","doi":"10.1016/j.genrep.2024.102007","DOIUrl":"10.1016/j.genrep.2024.102007","url":null,"abstract":"<div><p>Sweet sorghum (<em>Sorghum bicolor</em> (L.) Moench) is the only grain and stalk crop that can be used for multipurpose. Despite its global significance and potential, it faced genetic erosion. These are due to low productivity and lower farmers' preferences, which is not considered one of the most important cereal crops in Ethiopia. To utilize and popularize these crops, understanding the genetic diversity and population structure is a pre-request. Therefore, this study was aimed to assess the genetic diversity and population structure of selected 82 Ethiopian sweet sorghum accessions using 10 simple sequence repeat (SSR) markers that represent seven geographic regions of Ethiopia. The study revealed a total of 116 alleles with a mean of 11.6 alleles per locus. All used microsatellite loci were highly polymorphic with polymorphic information content (PIC) ranging from 0.75 to 0.90 with an average of 0.82. They showed high gene diversity ranging from 0.59 to 0.81 with an overall mean of 0.70. There was a moderate genetic differentiation (FST = 0.21) showing the presence of high gene flow (Nm = 5.033) where 91 % of the total variation was accounted for within populations genetic variability. The clustering, principal coordinate analysis (PCoA) and population structure did not cluster the studied populations into a separate group according to their geographical origin. In conclusion, the highest intra-population diversity was observed among populations of North Wollo (He = 0.81) and South Wollo (He = 0.79), and hence these areas can be considered as hot spots for the identification of novel traits. Therefore, the present study has generated baseline information for breeders to improve Ethiopian sweet sorghum through breeding, management, and conservation of the available genetic resources.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome analyses reveal selective signals in four Xinjiang cattle breeds","authors":"","doi":"10.1016/j.genrep.2024.102000","DOIUrl":"10.1016/j.genrep.2024.102000","url":null,"abstract":"<div><p>Xinjiang is home to three indigenous cattle breeds (Xinjiang Mongolian, Altay white-headed, and Kazakh cattle) and one crossbreed (Xinjiang Brown cattle), each possessing distinct and remarkable characteristics. In this study, we conducted comprehensive genome analyses of these four breeds in comparison with eight representative cattle breeds from around the world. Despite being predominantly <em>Bos taurus</em>, the proportion of <em>Bos indicus</em> ancestry in these indigenous breeds decreases with increasing latitude. This mixed genomic composition contributes to higher nucleotide diversity, lower linkage disequilibrium, and larger effective population sizes. Notably, Xinjiang Brown cattle exhibited higher LD at short distances, faster LD decay, and the largest effective population size, indicative of hybrid characteristics. Furthermore, we identified selective signals for lipids dynamics and coat colour in Altay white-headed cattle, immune resistance to local pathogens in Kazakh cattle, hydro-electrolyte balance and immune response in Xinjiang Mongolian cattle, and rapid growth and large body size in Xinjiang Brown cattle, as well as substance metabolism in three indigenous cattle. Our findings not only deepen the understanding of breed origins and diversity but also provide a foundation for exploring the genetic mechanisms underlying breed characteristics and facilitating further breed improvement.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141961427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment of the contribution of AGBL5 in autosomal recessive retinitis pigmentosa: Experience from an Iranian family evaluation and literature review","authors":"","doi":"10.1016/j.genrep.2024.102002","DOIUrl":"10.1016/j.genrep.2024.102002","url":null,"abstract":"<div><h3>Background</h3><p>Retinitis Pigmentosa (RP) as inherited disease of the retina causes vision impairment due to progressive abnormalities of photoreceptors or the retinal pigment epithelial cells. RP as a clinical heterogenous disorder characterized by wide genetic heterogeneity with a broad range of causative genes involved in the genesis of the disease. Pathogenic variants in AGBL5 have been reported in few cases with RP. The aim of this study is to identify the accurate clinical diagnosis of RP in an Iranian family based on the combination of clinical and genetic investigations.</p></div><div><h3>Materials and methods</h3><p>We used whole exome sequencing (WES) to identify the pathogenic genetic defect responsible for RP in an Iranian family with consanguineous marriage. Using various filtering steps, we filtered out the exome data to narrow down the annotated variants. Variant prioritization was done based on a panel of RP genes.</p></div><div><h3>Results</h3><p>All the annotated variants from WES analysis were passed through various filtering steps depending upon allelic frequency, genomic position, protein impact, pathogenic effect, previous relevance to the disease phenotype and quality of the variants. Finally, we found the nonsense homozygous change in <em>AGBL5</em> gene (NM_021831.6; c.1729C&gt;T; p.Arg577Ter). The RP phenotypes of the proband were similar to previous reports.</p></div><div><h3>Conclusion</h3><p>This study can provide further evidence regarding the relationship of pathogenic variants in <em>AGBL5</em> as a cause of RP and we believe that it can provide evidences for the relationship between clinical manifestations and pathogenic variants.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142077565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Y chromosome genes interplay with interval timing in regulating mating duration of male Drosophila melanogaster","authors":"","doi":"10.1016/j.genrep.2024.101999","DOIUrl":"10.1016/j.genrep.2024.101999","url":null,"abstract":"<div><p>We explore the understudied role of Y chromosome genes in modulating mating behaviors and interval timing in male fruit flies. Our findings reveal a significant impact of these genes on mating duration, a critical aspect of sexual selection and reproductive success. Through the use of XO males lacking a Y chromosome and RNA interference (RNAi) techniques to knockdown specific Y chromosome genes, we demonstrate that the Y chromosome and its genes <em>WDY</em> and <em>CCY</em> are essential for the generation of Longer-Mating-Duration (LMD) and Shorter-Mating-Duration (SMD) behaviors. Notably, the neuronal knockdown of <em>Ppr-Y</em>, a gene highly expressed in both neuronal and glial cells, leads to profound disruptions in courtship and mating behaviors without affecting fertility. Utilizing the fly SCope scRNA-seq data platform, we identified that several Y chromosome genes, including <em>kl-3</em>, <em>kl-5</em>, <em>WDY</em>, and <em>PRY</em>, are preferentially expressed in fru-positive neurons, suggesting a role in male-specific neuronal populations. Our work not only advances the understanding of the Y chromosome's contribution to complex mating behaviors but also sets the stage for future investigations into the molecular mechanisms underlying sexual dimorphism and reproductive strategies in <em>Drosophila</em>.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}